The latest investigation could severely weaken the agency.
The suspects represent half of the deputy chiefs at the Corruption Eradication Commission (KPK).
Last May, the head of the KPK, Antasari Azhar, was named a suspect in a murder investigation.
The KPK has been at the forefront of the fight against corruption in Southeast Asia's biggest economy.
Together with the corruption court, it has been responsible for the imprisonment of dozens of officials from central bankers to politicians.
Foreign investors expressed concern over the mounting tension between the KPK and the police, which is one of several institutions along with the judiciary, civil service and parliament that regularly rank among the most corrupt in the country.
"The anti-corruption drive is being politicised and investors will take a negative view on that," said James Bryson of HB Capital, which invests in Indonesian stocks.
The KPK is widely respected by the public because of its successes in investigating officials in a country which last year was ranked 126th out of 180 countries by the global corruption watchdog Transparency International.
Some analysts have said that the police are trying to undermine the KPK, which has investigated senior police officials in the past. Police officials have denied the allegations.
The police have for months privately hinted to reporters that they planned to detain one or more senior officials from the KPK, mentioning inappropriate use of wire-taps and instances of corruption.